I've got 8 100W solar panels, the cheap flexible kind. Dodger:
2 panels on starboard wired in series
2 panels on port wired in series
They connect under the dodger, and 1 pair of wires runs down to a bus bar that feeds the controller

Bimini:
2 panels on starboard wired in series
2 panels on port wired in series
They connect under the bimini, and 1 pair of wires runs down to a bus bar that feeds the controller

In the baja sun, with the sun almost at 90degrees these days, I still peak at around 30 amps, with an average daily charge of 2800wh.

After googling, reading, etc, I decided on this approach:
Run a second wire down on the dodger and bimini, so I can isolate port and starboard series pairs.
Setup a second 30amp controller, so I have a MPPT 30A on port and a MPPT 60A on starboard. Since the top is not flat, it's kinda rounded, I figure even in full sun with no obstructions, one side will be aimed slightly better at the sun than the other.

I figure the best option would be to run each pair in series to a controller, but I didn't want to fork out the money for 3 20A controllers, since the panels are 5.5amps each I figured 10A controllers would be too close for comfort.

Eventually I see me replacing the cheap flexible panels with better built glass panels, but until that happens I'm trying to get the most I can without spending too much $$$, since I'm out of work.

You may be peaking at whatever your batteries can accept at any given discharge rate....

Our W / A is about the same. PWM and two panels (one of which likely party shaded part of the day). So, in my book, your setup is about fine.

Or else your panels are just not up to the job?

In my own experience monocrystaline blacks are best value and cheap Chinese monos are second best. So I would not go the regulator way, but I could be tempted to buy 800$ on monocrystalines as a first step.

2800 wh equates to roughly 260 ah @ 12 v. On our boat in the SoC, that is more than our average daily load. Thus, sounds like your batteries are likely topped up and don't need more than 30 a. What's you batterymonitor telling you?

Typically I make just enough to top off the batteries every day, but if I do anything above basic life support, like make water, run the compressor to clean the bottom, etc, I put a hole in it. I never get the holes back, so I eventually have to charge with either the generator or the main engine.

I figured if I wire this up I can see if there's any measurable difference in performance, if there is, I can see about adding 2 more to get every panel pair in series on their own PPT. I wonder if there will be issues with multiple charge controllers trying to work at once.

If your getting 30 amps at peak sun, your getting most of what the panels will produce, in real life. Sure the name plate rating is 5.5 amps but that's in a lab, not in real life.

Factor 65% of rated capacity for average peak load with PWM and maybe 75% or so for MPPT. Your 30 amps is between those two numbers, so your doing pretty well.

If the cheap panels does not have a bypass diode, when one half of one cell of one panel of two in series is shaded your loosing about 80% ish of the output of both panels as the shaded cell acts as a resistor to voltage. If there is a bypass diode, you only loose the output of one panel.

Shading is a serious issue on a sailboat. So location, location location, and keeping shading down to a minimum. Running them all parallel, generally gives slightly better performance. But that's a bit contested sometimes.

Typically I make just enough to top off the batteries every day, but if I do anything above basic life support, like make water, run the compressor to clean the bottom, etc, I put a hole in it. I never get the holes back, so I eventually have to charge with either the generator or the main engine.

We have a victron battery monitor, that's where my 30 amps during peak periods comes from.

A peak of 30A from 800w of solar with the sun at close to 90į is not good. Check you are reading the solar panel output not the solar panel output minus the load, which is what the battery monitor will usually report. For example if the solar panels are putting out 40A and there is a 10A load from the fridge etc, the battery monitor will report +30A. In one hour it will only count +30 Ahrs. Not the 40A and 40 Ahrs that has been the true output of the panels. Some battery monitors will display the input and output separately, but most simply report the net gain or loss.

If the maximum output of the panel's is 30A and there is no regulation then there is a problem.

Two, or even multiple MPPT controllers only make a small difference to the output and your numbers (if your are reading the solar output correctly) suggest there is something fundamentally wrong such as a poor connection, a defective panel or maybe wiring that is woefully thin.

A clamp on multimeter is a good place to start. It can be used to check the output from each panel seperately. If there is a problem with a panel or with a connection it will show up as reduced current, which makes it easy to isolate where the problem is located. It can also be used to check the total output from all the panels rather than using the battery monitor display, which may be confusing things. Put on a high load when using the clamp-on meter so you can be sure that the controller is not in regulation mode.

A peak of 30A from 800w of solar with the sun at close to 90į is not good. Check you are reading the solar panel output not the solar panel output minus the load, which is what the battery monitor will usually report. For example if the solar panels are putting out 40A and there is a 10A load from the fridge etc, the battery monitor will report +30A. In one hour it will only count +30 Ahrs. Not the 40A and 40 Ahrs that has been the true output of the panels. Some battery monitors will display the input and output separately, but most simply report the net gain or loss.

Excellent point. I think you may have nailed it.

In which case, the OP is using more like 300Ah for his "basic life support"

I wonder if there will be issues with multiple charge controllers trying to work at once.

IMHO yes, if they work on the same bank.

I say this because even with our most basic pwm one (sunsei) it remembers yesterday's peak and low and will extend or cut off the bulk mode accordingly today. Now you may actually want to extend the bulk mode in most boat scenarios.

I imagine that more advanced regulators may have more advanced algorithms. (Leading to more advanced interference ...)

Some Victrons are programmable, then you can likely program them round some challenges.

Still, my take would be quality monocrystalines, wired and regulated in a pattern that minimises a/m effects of shade. Angle them if you can.

If you can easily afford an experiment though, why not play some, sure!

I have 3X240 panels and regularly see 60 AH output (maybe 2 out of 5 days depending on how much we have taken out the day/night before). Have a Morningstar MPPT 60A controller. One nice thing about Morningstars is that they log daily data internally and they have an ethernet connection. I can go back and check a dozen parameters by day since the install.

The comment about battery moniters only showing the net is spot on.

Regarding wiring, I wired my panels in parallel to avoid shade on one panel taking down the array. They are 35 volt (nominal) voltage and I used #4 wire from the panels to the controller.

Funny how you forget how much juice you use sometime but my panels have put out 240,000 AH in 4-1/2 years, and still going strong. Certainly cost beneficial vs. running a generator.

If you suspect one of the panels is not producing correctly try shading each panel with a light blocking item (rug or towel) and check your output reduction.
With your series linkup a dodgy panel should be obvious but if they were all in parallel you may not pick up the loss or partial loss of one panel.
Cheers